Once the observations are made, we must remove the instrumental signature, including atmospheric effects, as fully as possible. To use the observational data effectively, the reduction program must make correct assumptions about the way the data were gathered, and the way the instrument itself (including the atmosphere!) really works.
The atmospheric part can be removed quite accurately, but some remaining instrumental effects, due to a mismatch between the instrumental and standard passbands, cannot be completely removed, because some information is missing (especially in the conventional photometric systems). Nevertheless, if the filters are quite close to the standard ones, the missing information is fairly small, and good results are possible.
Again, interaction between the observer and the program is necessary, both to obtain the necessary information and to decide how to proceed when choices are not clear-cut. Safe defaults are offered to the beginner; more experienced observers can try various assumptions to see what works best for their purposes. In both programs, the goal is to allow a wide variety of choices, but to warn users of potential problems.